Analysis of monocyte data (SCZ vs CTR): simplest model (~ status)

Load data

DESeq2 anaylsis

We then go into the differential gene-expression analysis:

  1. Overview of the results

out of 24437 with nonzero total read count adjusted p-value < 0.1 LFC > 0 (up) : 26, 0.11% LFC < 0 (down) : 15, 0.061% outliers [1] : 0, 0% low counts [2] : 0, 0% (mean count < 0) [1] see ‘cooksCutoff’ argument of ?results [2] see ‘independentFiltering’ argument of ?results

As well as the number of differentially expressed genes at lfc </> -0.5/0.5 at padj < 0.1:

[1] 36

Interactive results table

  1. Results

Enrichment testing results

  1. List enrichments

[1] “Reminder: we have 17 upregulated and 8 downregulated genes.”

  1. GO enrichments

Signature co-variance

  1. Signature expression (Microglia, NfKB, IFNy)

(1A) Signature expression only for lFC < -1 | lfc > 1 genes (Microglia, NfKB, IFNy)

  1. Signature co-variance

[1] “Microglia”

[1] “NFKB”

[1] “IFNy”

(2A) Scatter plot of signature co-variance

(2A) Scatter plot of signature with DEG co-variance (messy, need to clean up)

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